Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions

This article reviews current methods for the reliable heterologous overexpression in Escherichia coli and purification of milligram quantities of bacterial membrane sensor kinase (MSK) proteins belonging to the two-component signal transduction family of integral membrane proteins. Many of these methods were developed at Leeds alongside Professor Steve Baldwin to whom this review is dedicated. It also reviews two biophysical methods that we have adapted successfully for studies of purified MSKs and other membrane proteins–synchrotron radiation circular dichroism (SRCD) spectroscopy and analytical ultracentrifugation (AUC), both of which are non-immobilization and matrix-free methods that require no labelling strategies. Other techniques such as isothermal titration calorimetry (ITC) also share these features but generally require high concentrations of material. In common with many other biophysical techniques, both of these biophysical methods provide information regarding membrane protein conformation, oligomerization state and ligand binding, but they possess the additional advantage of providing direct assessments of whether ligand binding interactions are accompanied by conformational changes. Therefore, both methods provide a powerful means by which to identify and characterize inhibitor binding and any associated protein conformational changes, thereby contributing valuable information for future drug intervention strategies directed towards bacterial MSKs.

[1]  L. Bubacco,et al.  Effects of Trehalose on Thermodynamic Properties of Alpha-synuclein Revealed through Synchrotron Radiation Circular Dichroism , 2015, Biomolecules.

[2]  E. Longo,et al.  Application of circular dichroism and magnetic circular dichroism for assessing biopharmaceuticals formulations photo-stability and small ligands binding properties. , 2015, International journal of pharmaceutics.

[3]  Bill C. A. Pulford,et al.  CDApps: integrated software for experimental planning and data processing at beamline B23, Diamond Light Source , 2015, Journal of synchrotron radiation.

[4]  G. Siligardi,et al.  CD spectroscopy: an essential tool for quality control of protein folding. , 2015, Methods in molecular biology.

[5]  R. Owens Structural Proteomics , 2015, Methods in Molecular Biology.

[6]  D. Svergun,et al.  A coiled-coil domain acts as a molecular ruler in LPS chain length regulation , 2014, Nature Structural &Molecular Biology.

[7]  K. Gardner,et al.  Full-length structure of a monomeric histidine kinase reveals basis for sensory regulation , 2014, Proceedings of the National Academy of Sciences.

[8]  C. F. van der Walle,et al.  The effect of palmitoylation on the conformation and physical stability of a model peptide hormone. , 2014, International journal of pharmaceutics.

[9]  L. Bubacco,et al.  Ceftriaxone blocks the polymerization of α-synuclein and exerts neuroprotective effects in vitro. , 2014, ACS chemical neuroscience.

[10]  Peter Schuck,et al.  SEDFIT-MSTAR: molecular weight and molecular weight distribution analysis of polymers by sedimentation equilibrium in the ultracentrifuge. , 2014, The Analyst.

[11]  Gwyndaf Evans,et al.  Membrane protein structure determination — The next generation☆☆☆ , 2014, Biochimica et biophysica acta.

[12]  M. Phillips-Jones,et al.  Ligand- and drug-binding studies of membrane proteins revealed through circular dichroism spectroscopy. , 2014, Biochimica et biophysica acta.

[13]  Karl A. Hassan,et al.  Transcriptomic and biochemical analyses identify a family of chlorhexidine efflux proteins , 2013, Proceedings of the National Academy of Sciences.

[14]  H. Choudhury,et al.  Functional Characterization of SbmA, a Bacterial Inner Membrane Transporter Required for Importing the Antimicrobial Peptide Bac7(1-35) , 2013, Journal of bacteriology.

[15]  Arthur J. Rowe,et al.  MultiSig: a new high-precision approach to the analysis of complex biomolecular systems , 2013, European Biophysics Journal.

[16]  Small molecules interacting with α-synuclein: antiaggregating and cytoprotective properties , 2013, Amino Acids.

[17]  Stephen E. Harding,et al.  Hydrodynamic modelling of protein conformation in solution: ELLIPS and HYDRO , 2013, Biophysical Reviews.

[18]  P. Henderson,et al.  A systematic approach to the amplified expression, functional characterization and purification of inositol transporters from Bacillus subtilis , 2013, Molecular membrane biology.

[19]  J. Nakayama,et al.  Interactions of the intact FsrC membrane histidine kinase with the tricyclic peptide inhibitor siamycin I revealed through synchrotron radiation circular dichroism. , 2013, Physical chemistry chemical physics : PCCP.

[20]  R. Viola,et al.  Detergent selection for enhanced extraction of membrane proteins. , 2012, Protein expression and purification.

[21]  J. Kirby,et al.  Genetic and Biochemical Dissection of a HisKA Domain Identifies Residues Required Exclusively for Kinase and Phosphatase Activities , 2012, PLoS genetics.

[22]  Pikyee Ma,et al.  Interactions of the intact FsrC membrane histidine kinase with its pheromone ligand GBAP revealed through synchrotron radiation circular dichroism. , 2012, Biochimica et biophysica acta.

[23]  T. Jávorfi,et al.  8.23 Spectroscopic Analysis: Synchrotron Radiation Circular Dichroism , 2012 .

[24]  T. Jávorfi,et al.  Circular dichroism beamline B23 at the Diamond Light Source. , 2012, Journal of synchrotron radiation.

[25]  Peter Schuck,et al.  Extended Fujita approach to the molecular weight distribution of polysaccharides and other polymeric systems. , 2011, Methods.

[26]  M. Schilstra,et al.  Chapter 7:Circular Dichroism , 2011 .

[27]  S. Harding,et al.  Insight into protein-protein interactions from analytical ultracentrifugation. , 2010, Biochemical Society transactions.

[28]  Pikyee Ma Structure-activity relationships of membrane proteins:the NCS1 family of transporters and sensor kinases of two component systems , 2010 .

[29]  T. Jávorfi,et al.  Measuring circular dichroism in a capillary cell using the b23 synchrotron radiation CD beamline at diamond light source. , 2010, Chirality.

[30]  Pikyee Ma,et al.  Expression, purification and activities of the entire family of intact membrane sensor kinases from Enterococcus faecalis , 2008, Molecular membrane biology.

[31]  T. Mascher,et al.  Stimulus Perception in Bacterial Signal-Transducing Histidine Kinases , 2006, Microbiology and Molecular Biology Reviews.

[32]  M. Williamson,et al.  Redox‐responsive in vitro modulation of the signalling state of the isolated PrrB sensor kinase of Rhodobacter sphaeroides NCIB 8253 , 2006, FEBS letters.

[33]  C. Bauer,et al.  Identification of a Ubiquinone-binding Site That Affects Autophosphorylation of the Sensor Kinase RegB* , 2006, Journal of Biological Chemistry.

[34]  Wayne A Hendrickson,et al.  Structure of the entire cytoplasmic portion of a sensor histidine‐kinase protein , 2005, The EMBO journal.

[35]  D. Scott,et al.  Correcting for the Buoyancy of Macromolecules: Density Increments and Apparent Partial Specific Volumes with ParticularReference to the Study of Membrane Proteins , 2005 .

[36]  F. Guerlesquin,et al.  A copper protein and a cytochrome bind at the same site on bacterial cytochrome c peroxidase. , 2004, Biochemistry.

[37]  Paul Curnow,et al.  Membrane proteins, lipids and detergents: not just a soap opera. , 2004, Biochimica et biophysica acta.

[38]  S. Kaplan,et al.  Reconstitution of the Rhodobacter sphaeroides cbb3-PrrBA signal transduction pathway in vitro. , 2004, Biochemistry.

[39]  P. Bird,et al.  Production of serpins using yeast expression systems. , 2004, Methods.

[40]  N. Sreerama,et al.  On the analysis of membrane protein circular dichroism spectra , 2004, Protein science : a publication of the Protein Society.

[41]  P. Schuck,et al.  Calculating sedimentation coefficient distributions by direct modeling of sedimentation velocity concentration profiles. , 2004, Methods in enzymology.

[42]  P. Henderson,et al.  Collection and characterisation of bacterial membrane proteins , 2003, FEBS letters.

[43]  P. Schuck On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation. , 2003, Analytical biochemistry.

[44]  N. C. Price,et al.  Identification of Oligomerization and Drug-binding Domains of the Membrane Fusion Protein EmrA* , 2003, The Journal of Biological Chemistry.

[45]  J. Stock,et al.  Histidine protein kinases: key signal transducers outside the animal kingdom , 2002, Genome Biology.

[46]  C. A. Potter,et al.  Expression, purification and characterisation of full-length heterologously expressed histidine protein kinase RegB from Rhodobacter sphaeroides , 2002 .

[47]  M. Williamson,et al.  Expression, purification and characterisation of full-length histidine protein kinase RegB from Rhodobacter sphaeroides. , 2002, Journal of molecular biology.

[48]  L. Pearl,et al.  Regulation of Hsp90 ATPase Activity by the Co-chaperone Cdc37p/p50 cdc37 * , 2002, The Journal of Biological Chemistry.

[49]  Ann M Stock,et al.  Histidine kinases and response regulator proteins in two-component signaling systems. , 2001, Trends in biochemical sciences.

[50]  D. Winzor,et al.  Sedimentation velocity analytical ultracentrifugation , 2001 .

[51]  B. Poolman,et al.  The amplified expression, identification, putrification, assay and properties of his-tagged bacterial membrane transport proteins , 2000 .

[52]  M. Inouye,et al.  Histidine kinases: diversity of domain organization , 1999, Molecular microbiology.

[53]  Victoria A. Feher,et al.  Two-Component Signal Transduction in Bacillus subtilis: How One Organism Sees Its World , 1999, Journal of bacteriology.

[54]  J. Boulter,et al.  Hydrodynamic properties of human erythrocyte band 3 solubilized in reduced Triton X-100. , 1999, Biophysical journal.

[55]  M. Simon,et al.  Structure of CheA, a Signal-Transducing Histidine Kinase , 1999, Cell.

[56]  G. Siligardi,et al.  Biomolecules interactions and competitions by non-immobilised ligand interaction assay by circular dichroism. , 1998, Enantiomer.

[57]  J. Boulter,et al.  Ultracentrifugation studies on the transmembrane domain of the human erythrocyte anion transporter Band 3 in the detergent C12E8 , 1998, European Biophysics Journal.

[58]  A. Barclay,et al.  Characterisation of the low affinity interaction between rat cell adhesion molecules CD2 and CD48 by analytical ultracentrifugation , 1997, European Biophysics Journal.

[59]  J. Boulter,et al.  Hydrodynamic examination of the dimeric cytoplasmic domain of the human erythrocyte anion transporter, band 3. , 1996, Biophysical journal.

[60]  J. Casey,et al.  Purification and characterization of band 3 protein. , 1989, Methods in enzymology.

[61]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[62]  E. Degenkolb,et al.  Kinetics of carboxymyoglobin and oxymyoglobin studied by picosecond spectroscopy. , 1979, Biophysical journal.